This feature has been replaced and improved!

Neurolucida 360 software, version 2020 and later, includes a new Subvolume tool that simplifies the process of dividing large and/or complex image volumes into smaller, more manageable "chunks" to facilitate tracing.

Large volume reconstruction

Goal

Create a large reconstruction from a very large image volume (i.e., big data) using one of the three 3D tracing modes. This is especially useful when you have images that are too large to load and manipulate efficiently in 3D.

Principle

While the entire image volume is available for reconstruction, you have the ability to define subvolumes based on the structures you want to trace, trace each subvolume's structures in 3D, then obtain a single data file that combines the 3D data from the subvolumes.

Procedure

  1. Create a new profile so that you can easily return to your traces at a later time:
    • File>User profile, click New profile and use Image name as profile name.
  2. In the Workspace ribbon, click the Reconstruction button.
  3. In the Large volume settings window:
    1. Select the desired image stack.
    2. Enter the dimensions for display.

      Choose a display size small enough to obtain a subvolume that will be highly responsive when tracing.

    3. The center of the image volume is displayed in the Tracing window. Z meter, Macro View and Large Volume Reconstruction windows open.
  4. Open the 3D environment, resize it and position it in such a way that you can comfortably trace in the 3D environment while keeping the other windows visible. For example, if you're using docked windows:
  5. Define the dimensions for AutoMove: In the Workspace ribbon, click Define AutoMove and drag the sides of the AutoMove rectangle to resize it.

    Movement is associated with AutoMove by default in Large Volume Reconstruction mode.

  6. Click in Macro View to navigate to a specific area. The area is displayed in the Tracing window.

    The black rectangle represents the display rectangle defined in the Large volume settings window.

  7. In the Large volume reconstruction window:
    1. Specify the subvolume height and location: Scroll the mouse wheel to navigate to the top of the subvolume and click Set; scroll the mouse wheel to the bottom and click Set. To change the mouse wheel settings (i.e., number of planes per click), use the slider.

      Setting the top and bottom of the subvolume is the default method. To use a different method, click the "cog" button.

    2. Adjust the image settings in the histogram.

      If you're working with a multichannel image, make sure that the correct channels are selected before you generate the subvolume. To de-select a channel, uncheck the corresponding box in the Include column.

    3. Optional: To refine the subvolume center X, Y or Z, in the Navigation section, enter values under desired: and click the Change location button.
    4. Click the Reconstruct subvolume button to generate the subvolume and display it in the 3D environment.

      Passing the subvolume on to the 3D environment may take a while. You can keep track of the operation progress in the status bar at the bottom of the screen.

  8. Trace the structures as desired:
    1. In the 3D environment, detect somas as needed.
    2. Trace the structures using one of the three tracing modes (user-guided, smart manual, automatic).
    3. Detect varicosities, spines and synapses as needed.
  9. Return to the Large volume reconstruction window and click Show large volume.
  10. Repeat steps 4-8 as necessary to trace all structures of interest.
    • In Macro View, you'll notice aqua blue rectangles in addition to the black rectangle. The aqua blue rectangles represent the subvolumes that you've already worked on; the black rectangle represents the current subvolume.
    • To change the display dimensions of the subvolume, click the cog button under the Reconstruction button.
  11. Save the data file (File>Save).

The next time you open Neurolucida 360 software with the same profile, the Large Volume Reconstruction mode will be on by default. Turn it off (click the Reconstruction button in the Workspace ribbon) if you want to load images other than the large image volume.